Ef: A Fairy Tale of the Two. consists of two parts with three chapters each. The first part is titled Ef: The First Tale. and primarily consists of the story of Hiro Hirono, Miyako Miyamura, Kyosuke Tsutsumi, Kei Shindo, and Yuko Amamiya. It consists of a prologue and two main chapters with Miyako as the focus for the first chapter, and Kei for the second.

This is followed by the second part of the story,Ef: The Latter Tale., which primarily deals with the story of Renji Aso, Chihiro Shindo, Shuichi Kuze, Mizuki Hayama, and Yu Himura. The second part consists of two more main chapters and an ending chapter, with Chihiro as the focus for the third chapter, and Mizuki for the fourth. Bringing the two parts together forms the all-encompassing Ef: A Fairy Tale of the Two..The story is set in the town Otowa(音羽).